-
1
-
-
0003903126
-
-
Springer-Verlag, New York
-
van Holde KE (1989) Chromatin, Springer-Verlag, New York.
-
(1989)
Chromatin
-
-
van Holde, K.E.1
-
2
-
-
0035704707
-
Role of DNA sequence in nucleosome stability and dynamics
-
Widom J (2001) Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys 34: 269-324.
-
(2001)
Q Rev Biophys
, vol.34
, pp. 269-324
-
-
Widom, J.1
-
3
-
-
60349089645
-
Nucleosome positioning and gene regulation: Advances through genomics
-
10: 161-172
-
Jiang CZ, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 3: 358-U327.10: 161-172.
-
(2009)
Nat Rev Genet
, vol.3
-
-
Jiang, C.Z.1
Pugh, B.F.2
-
4
-
-
22744432660
-
Genome-scale identification of nucleosome positions in S-cerevisiae
-
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale identification of nucleosome positions in S-cerevisiae. Science 309: 626-630.
-
(2005)
Science
, vol.309
, pp. 626-630
-
-
Yuan, G.C.1
Liu, Y.J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
-
5
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
Qi, J.4
Zanton, S.J.5
-
6
-
-
34748826166
-
A high- resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high- resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
-
(2007)
Nat Genet
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
-
7
-
-
33947514987
-
Sequence-directed mapping of nucleosome positions
-
Salih F, Salih B, Trifonov EN (2007) Sequence-directed mapping of nucleosome positions. J Biomol Struct Dyn 24: 489-493.
-
(2007)
J Biomol Struct Dyn
, vol.24
, pp. 489-493
-
-
Salih, F.1
Salih, B.2
Trifonov, E.N.3
-
8
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
-
9
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich TN, Jiang CZ, Ioshikhes IP, Li XY, Venters BJ, et al. (2008) Nucleosome organization in the Drosophila genome. Nature 45.
-
(2008)
Nature
, pp. 45
-
-
Mavrich, T.N.1
Jiang, C.Z.2
Ioshikhes, I.P.3
Li, X.Y.4
Venters, B.J.5
-
10
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui KR, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.R.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
-
11
-
-
46449103738
-
A highresolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, et al. (2008) A highresolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063.
-
(2008)
Genome Res
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
-
12
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-U129.
-
(2009)
Nature
, vol.458
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
-
13
-
-
68249142923
-
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
-
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, et al. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-U870.
-
(2009)
Nat Struct Mol Biol
, vol.16
-
-
Zhang, Y.1
Moqtaderi, Z.2
Rattner, B.P.3
Euskirchen, G.4
Snyder, M.5
-
14
-
-
74949110964
-
Highresolution nucleosome mapping reveals transcription-dependent promoter packaging
-
Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N (2010) Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90-100.
-
(2010)
Genome Res
, vol.20
, pp. 90-100
-
-
Weiner, A.1
Hughes, A.2
Yassour, M.3
Rando, O.J.4
Friedman, N.5
-
15
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
16
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal E, Fondufe-Mittendorf Y, Chen LY, Thastrom A, Field Y, et al. (2006) A genomic code for nucleosome positioning. Nature 442: 772-778.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.Y.3
Thastrom, A.4
Field, Y.5
-
17
-
-
43149114926
-
Re-cracking the nucleosome positioning code
-
Article 14
-
Segal MR (2008) Re-cracking the nucleosome positioning code. Stat Appl Genet Mol Biol 7: Article 14.
-
(2008)
Stat Appl Genet Mol Biol
, vol.7
-
-
Segal, M.R.1
-
18
-
-
15744397041
-
Chromatin remodeling complexes: Strength in diversity, precision through specialization
-
Cairns BR (2005) Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr Opin Genet Dev 15: 185-190.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 185-190
-
-
Cairns, B.R.1
-
19
-
-
33847065486
-
The epigenomics of cancer
-
Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128: 683-692.
-
(2007)
Cell
, vol.128
, pp. 683-692
-
-
Jones, P.A.1
Baylin, S.B.2
-
20
-
-
34547890019
-
Functions of site-specific histone acerylation and deacetylation
-
Shahbazian MD, Grunstein M (2007) Functions of site-specific histone acerylation and deacetylation. Annu Rev Biochem 76: 75-100.
-
(2007)
Annu Rev Biochem
, vol.76
, pp. 75-100
-
-
Shahbazian, M.D.1
Grunstein, M.2
-
21
-
-
53249133260
-
Control of nucleosome positions by DNA sequence and remodeling machines
-
Schnitzler GR (2008) Control of nucleosome positions by DNA sequence and remodeling machines. Cell Biochem Biophys 51: 67-80.
-
(2008)
Cell Biochem Biophys
, vol.51
, pp. 67-80
-
-
Schnitzler, G.R.1
-
22
-
-
33745847547
-
Antagonistic forces that position nucleosomes in vivo
-
Whitehouse I, Tsukiyama T (2006) Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol 13: 633-640.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 633-640
-
-
Whitehouse, I.1
Tsukiyama, T.2
-
23
-
-
33749406106
-
Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters
-
Hogan GJ, Lee CK, Lieb JD (2006) Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2: 1433-1450.
-
(2006)
PLoS Genet
, vol.2
, pp. 1433-1450
-
-
Hogan, G.J.1
Lee, C.K.2
Lieb, J.D.3
-
24
-
-
0018372296
-
Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones
-
Rhodes D (1979) Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucl Acids Res 6: 1805-1816.
-
(1979)
Nucl Acids Res
, vol.6
, pp. 1805-1816
-
-
Rhodes, D.1
-
25
-
-
0011031885
-
Naturally-occurring poly (dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast
-
Struhl K (1985) Naturally-occurring poly (dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA 82: 8419-8423.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 8419-8423
-
-
Struhl, K.1
-
26
-
-
60349115060
-
Poly(dA:DT) tracts: Major determinants of nucleosome organization
-
Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 65-71
-
-
Segal, E.1
Widom, J.2
-
27
-
-
63449105244
-
Intrinsic variability of gene expression encoded in nucleosome positioning sequences
-
Choi JK, Kim YJ (2009) Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 41: 498-503.
-
(2009)
Nat Genet
, vol.41
, pp. 498-503
-
-
Choi, J.K.1
Kim, Y.J.2
-
28
-
-
0001415964
-
The pitch of chromatin DNA is reflected in its nucleotide-sequence
-
Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide-sequence. Proc Natl Acad Sci USA 77: 3816-3820.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 3816-3820
-
-
Trifonov, E.N.1
Sussman, J.L.2
-
29
-
-
33749153628
-
Nucleosome positions predicted through comparative genomics
-
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF (2006) Nucleosome positions predicted through comparative genomics. Nat Genet 38: 1210-1215.
-
(2006)
Nat Genet
, vol.38
, pp. 1210-1215
-
-
Ioshikhes, I.P.1
Albert, I.2
Zanton, S.J.3
Pugh, B.F.4
-
30
-
-
45849135627
-
Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions
-
Liu HD, Wu JS, Xie JM, Yang XN, Lu ZH, et al. (2008) Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions. Biophys J 94: 4597-4604.
-
(2008)
Biophys J
, vol.94
, pp. 4597-4604
-
-
Liu, H.D.1
Wu, J.S.2
Xie, J.M.3
Yang, X.N.4
Lu, Z.H.5
-
31
-
-
0024297584
-
The terminus of SV40 DNA-replication and transcription contains a sharp sequence-directed curve
-
Hsieh CH, Griffith JD (1988) The terminus of SV40 DNA-replication and transcription contains a sharp sequence-directed curve. Cell 52: 535-544.
-
(1988)
Cell
, vol.52
, pp. 535-544
-
-
Hsieh, C.H.1
Griffith, J.D.2
-
32
-
-
0025690307
-
Attraction, phasing and neighbor effects of histone octamers on curved DNA
-
Costanzo G, Dimauro E, Salina G, Negri R (1990) Attraction, phasing and neighbor effects of histone octamers on curved DNA. J Mol Biol 216: 363-374.
-
(1990)
J Mol Biol
, vol.216
, pp. 363-374
-
-
Costanzo, G.1
Dimauro, E.2
Salina, G.3
Negri, R.4
-
33
-
-
0033578872
-
Selective nucleosome disruption by drugs that bind in the minor groove of DNA
-
Fitzgerald DJ, Anderson JN (1999) Selective nucleosome disruption by drugs that bind in the minor groove of DNA. J Biol Chem 274: 27128-27138.
-
(1999)
J Biol Chem
, vol.274
, pp. 27128-27138
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
34
-
-
1042267433
-
Dual role of sequence-dependent DNA curvature in nucleosome stability: The critical test of highly bent Crithidia fasciculata DNA tract
-
Scipioni A, Pisano S, Anselmi C, Savino M, De Santis P (2004) Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract. Biophys Chem 107: 7-17.
-
(2004)
Biophys Chem
, vol.107
, pp. 7-17
-
-
Scipioni, A.1
Pisano, S.2
Anselmi, C.3
Savino, M.4
de Santis, P.5
-
35
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675.
-
(1986)
J Mol Biol
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
36
-
-
0032760667
-
DNA distortion as a factor in nucleosome positioning
-
Fitzgerald DJ, Anderson JN (1999) DNA distortion as a factor in nucleosome positioning. J Mol Biol 293: 477-491.
-
(1999)
J Mol Biol
, vol.293
, pp. 477-491
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
37
-
-
34447643262
-
Nucleosome positioning determinants
-
Fernandez AG, Anderson JN (2007) Nucleosome positioning determinants. JMol Biol 371: 649-668.
-
(2007)
JMol Biol
, vol.371
, pp. 649-668
-
-
Fernandez, A.G.1
Anderson, J.N.2
-
38
-
-
34447627286
-
DNA structural and sequence determinants for nucleosome positioning
-
Fitzgerald DJ, Anderson JN (1999) DNA structural and sequence determinants for nucleosome positioning. Gene Ther Mol Biol 4: 349-362.
-
(1999)
Gene Ther Mol Biol
, vol.4
, pp. 349-362
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
39
-
-
0024373679
-
DNA conformation and protein-binding
-
Travers AA (1989) DNA conformation and protein-binding. Annu Rev Biochem 58: 427-452.
-
(1989)
Annu Rev Biochem
, vol.58
, pp. 427-452
-
-
Travers, A.A.1
-
40
-
-
0038226895
-
DNA sequence and structure: Direct and indirect recognition in protein-DNA binding
-
Steffen NR, Murphy SD, Tolleri L, Hatfield GW, Lathrop RH (2002) DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics 18 Suppl 1: S22-30.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Steffen, N.R.1
Murphy, S.D.2
Tolleri, L.3
Hatfield, G.W.4
Lathrop, R.H.5
-
41
-
-
60849083224
-
Sequence-dependent Nucleosome Positioning
-
Chung HR, Vingron M (2009) Sequence-dependent Nucleosome Positioning. J Mol Biol 386: 1411-1422.
-
(2009)
J Mol Biol
, vol.386
, pp. 1411-1422
-
-
Chung, H.R.1
Vingron, M.2
-
42
-
-
0028225644
-
The crystal-structure of C-C-A-T-T-A-A-T-G-G - implications for bending of B-DNA at T-A steps
-
Goodsell DS, Kaczorgrzeskowiak M, Dickerson RE (1994) The crystal-structure of C-C-A-T-T-A-A-T-G-G - implications for bending of B-DNA at T-A steps. J Mol Biol 239: 79-96.
-
(1994)
J Mol Biol
, vol.239
, pp. 79-96
-
-
Goodsell, D.S.1
Kaczorgrzeskowiak, M.2
Dickerson, R.E.3
-
43
-
-
3142518260
-
Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
-
El Hassan MA, Calladine CR (1997) Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil Trans R Soc Lond Ser A-Math Phys Eng Sci 355: 43-100.
-
(1997)
Phil Trans R Soc Lond Ser A-Math Phys Eng Sci
, vol.355
, pp. 43-100
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
44
-
-
0034614483
-
Sequence-dependent DNA structure: Dinucleotide conformational maps
-
Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: Dinucleotide conformational maps. J Mol Biol 295: 71-83.
-
(2000)
J Mol Biol
, vol.295
, pp. 71-83
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
45
-
-
0026059567
-
Structure of the B-DNA decamer CC- A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-AG- A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
-
Prive GG, Yanagi K, Dickerson RE (1991) Structure of the B-DNA decamer CC- A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-AG- A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J Mol Biol 217: 177-199.
-
(1991)
J Mol Biol
, vol.217
, pp. 177-199
-
-
Prive, G.G.1
Yanagi, K.2
Dickerson, R.E.3
-
46
-
-
0029968821
-
Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes
-
Urpi L, Tereshko V, Malinina L, HuynhDinh T, Subirana JA (1996) Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes. Nat Struct Biol 3: 325-328.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 325-328
-
-
Urpi, L.1
Tereshko, V.2
Malinina, L.3
Huynhdinh, T.4
Subirana, J.A.5
-
47
-
-
0034614487
-
Sequence-dependent DNA structure: Tetranucleotide conformational maps
-
Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: Tetranucleotide conformational maps. J Mol Biol 295: 85-103.
-
(2000)
J Mol Biol
, vol.295
, pp. 85-103
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
48
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-U1281.
-
(2009)
Nature
, vol.461
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
-
49
-
-
0039837085
-
Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
-
Thastrom A, Lowary PT, Widlund HR, Cao H, Kubista M, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol 288: 213-229.
-
(1999)
J Mol Biol
, vol.288
, pp. 213-229
-
-
Thastrom, A.1
Lowary, P.T.2
Widlund, H.R.3
Cao, H.4
Kubista, M.5
-
50
-
-
1942489758
-
Nucleosomal locations of dominant DNA sequence motifs for histone - DNA interactions and nucleosome positioning
-
Thastrom A, Bingham LM, Widom J (2004) Nucleosomal locations of dominant DNA sequence motifs for histone - DNA interactions and nucleosome positioning. J Mol Biol 338: 695-709.
-
(2004)
J Mol Biol
, vol.338
, pp. 695-709
-
-
Thastrom, A.1
Bingham, L.M.2
Widom, J.3
-
51
-
-
0023777538
-
Statistical Distributions of Nucleosomes - Nonrandom Locations by a Stochastic Mechanism
-
Kornberg RD, Stryer L (1988) Statistical Distributions of Nucleosomes - Nonrandom Locations by a Stochastic Mechanism. Nucl Acids Res 16: 6677-6690.
-
(1988)
Nucl Acids Res
, vol.16
, pp. 6677-6690
-
-
Kornberg, R.D.1
Stryer, L.2
-
53
-
-
0028129558
-
Conserved patterns of bending in satellite and nucleosome positioning DNA
-
Fitzgerald DJ, Dryden GL, Bronson EC, Williams JS, Anderson JN (1994) Conserved patterns of bending in satellite and nucleosome positioning DNA. J Biol Chem 269: 21303-21314.
-
(1994)
J Biol Chem
, vol.269
, pp. 21303-21314
-
-
Fitzgerald, D.J.1
Dryden, G.L.2
Bronson, E.C.3
Williams, J.S.4
Anderson, J.N.5
-
54
-
-
0032103910
-
Unique translational positioning of nucleosomes on synthetic DNAs
-
Fitzgerald DJ, Anderson JN (1998) Unique translational positioning of nucleosomes on synthetic DNAs. Nucl Acids Res 26: 2526-2535.
-
(1998)
Nucl Acids Res
, vol.26
, pp. 2526-2535
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
55
-
-
0022477409
-
DNA bending at adenine thymine tracts
-
Koo HS, Wu HM, Crothers DM (1986) DNA bending at adenine thymine tracts. Nature 320: 501-506.
-
(1986)
Nature
, vol.320
, pp. 501-506
-
-
Koo, H.S.1
Wu, H.M.2
Crothers, D.M.3
-
56
-
-
34547643563
-
Nucleosome positioning signals in genomic DNA
-
Peckham HE, Thurman RE, Fu YT, Stamatoyannopoulos JA, Noble WS, et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17: 1170-1177.
-
(2007)
Genome Res
, vol.17
, pp. 1170-1177
-
-
Peckham, H.E.1
Thurman, R.E.2
Fu, Y.T.3
Stamatoyannopoulos, J.A.4
Noble, W.S.5
-
57
-
-
57149119464
-
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals. Plos Comput Biol 4: 25.
-
(2008)
Plos Comput Biol
, vol.4
, pp. 25
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
-
58
-
-
74949115966
-
Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC?
-
Hughes A, Rando OJ (2009) Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC? J Biol 8: 96.
-
(2009)
J Biol
, vol.8
, pp. 96
-
-
Hughes, A.1
Rando, O.J.2
-
59
-
-
75149135277
-
G plus C content dominates intrinsic nucleosome occupancy
-
Tillo D, Hughes TR (2009) G plus C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 13.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 13
-
-
Tillo, D.1
Hughes, T.R.2
-
60
-
-
77949393272
-
High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
-
Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, et al. (2010) High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences. Plos One 5: 5.
-
(2010)
Plos One
, vol.5
, pp. 5
-
-
Tillo, D.1
Kaplan, N.2
Moore, I.K.3
Fondufe-Mittendorf, Y.4
Gossett, A.J.5
-
61
-
-
0042386600
-
Sequencedependent DNA structure: A database of octamer structural parameters
-
Gardiner EJ, Hunter CA, Packer MJ, Palmer DS, Willett P (2003) Sequencedependent DNA structure: A database of octamer structural parameters. J Mol Biol 332: 1025-1035.
-
(2003)
J Mol Biol
, vol.332
, pp. 1025-1035
-
-
Gardiner, E.J.1
Hunter, C.A.2
Packer, M.J.3
Palmer, D.S.4
Willett, P.5
-
62
-
-
28444490422
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
-
Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, et al. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J 89: 3721-3740.
-
(2005)
Biophys J
, vol.89
, pp. 3721-3740
-
-
Dixit, S.B.1
Beveridge, D.L.2
Case, D.A.3
Cheatham, T.E.4
Giudice, E.5
-
63
-
-
34147191973
-
DNA stretching and extreme kinking in the nucleosome core
-
Ong MS, Richmond TJ, Davey CA (2007) DNA stretching and extreme kinking in the nucleosome core. J Mol Biol 368: 1067-1074.
-
(2007)
J Mol Biol
, vol.368
, pp. 1067-1074
-
-
Ong, M.S.1
Richmond, T.J.2
Davey, C.A.3
-
64
-
-
70449702038
-
A translational signature for nucleosome positioning in vivo
-
Caserta M, Agricola E, Churcher M, Hiriart E, Verdone L, et al. (2009) A translational signature for nucleosome positioning in vivo. Nucl Acids Res 37: 5309-5321.
-
(2009)
Nucl Acids Res
, vol.37
, pp. 5309-5321
-
-
Caserta, M.1
Agricola, E.2
Churcher, M.3
Hiriart, E.4
Verdone, L.5
-
65
-
-
0021760689
-
Structure of nucleosome core particle at 7A resolution
-
Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A (1984) Structure of nucleosome core particle at 7A resolution. Nature 311: 532-537.
-
(1984)
Nature
, vol.311
, pp. 532-537
-
-
Richmond, T.J.1
Finch, J.T.2
Rushton, B.3
Rhodes, D.4
Klug, A.5
-
66
-
-
0028264042
-
Human-Immunodeficiency-Virus integrase directs integration to sites of severe DNA distortion within the nucleosome core
-
Pruss D, Bushman FD, Wolffe AP (1994) Human-Immunodeficiency-Virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc Natl Acad Sci USA 91: 5913-5917.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 5913-5917
-
-
Pruss, D.1
Bushman, F.D.2
Wolffe, A.P.3
-
67
-
-
59649112972
-
Highresolution dynamic mapping of histone-DNA interactions in a nucleosome
-
Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, et al. (2009) Highresolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol 16: 124-129.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 124-129
-
-
Hall, M.A.1
Shundrovsky, A.2
Bai, L.3
Fulbright, R.M.4
Lis, J.T.5
-
68
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
69
-
-
34447644439
-
A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning
-
Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB (2007) A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning. J Mol Biol 371: 725-738.
-
(2007)
J Mol Biol
, vol.371
, pp. 725-738
-
-
Tolstorukov, M.Y.1
Colasanti, A.V.2
McCandlish, D.M.3
Olson, W.K.4
Zhurkin, V.B.5
-
70
-
-
67749086828
-
Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence
-
van Vugt JJFA, de Jager M, Murawska M, Brehm A, van Noort J, et al. (2009) Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS ONE 4: e6345.
-
(2009)
PLoS ONE
, vol.4
-
-
van Vugt, J.J.F.A.1
de Jager, M.2
Murawska, M.3
Brehm, A.4
van Noort, J.5
-
71
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
72
-
-
0025681521
-
Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA
-
Lowman H, Bina M (1990) Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA. Biopolymers 30: 861-876.
-
(1990)
Biopolymers
, vol.30
, pp. 861-876
-
-
Lowman, H.1
Bina, M.2
|